If you ask me, I would not delete item ledger entries, I would create a boolean field in Item ledger entry and mark it and leave it alone and differentiate these transactions from the rest. If you are cleaning up ledger entries then you need to make sure you remove all the related tables and sometimes you don't know where the transactions will refer back to ledger entries.

Deleting some entries is definately a no-go.
All entries, perhaps.
But no some.

I would do it like this:
* create a new company.

* import master-data from the old company.

* import relevant ledger entries into at General Journal Batch and post it.
Here you have to take into account(...) that posting customers and vendors will also create entries in G/L; and therefore you must not import G/L entries from Receiveables- and Payables Accounts.
Also think about VAT-accounts.